@inproceedings{1511,
  abstract     = {The fact that the complete graph K_5 does not embed in the plane has been generalized in two independent directions. On the one hand, the solution of the classical Heawood problem for graphs on surfaces established that the complete graph K_n embeds in a closed surface M if and only if (n-3)(n-4) is at most 6b_1(M), where b_1(M) is the first Z_2-Betti number of M. On the other hand, Van Kampen and Flores proved that the k-skeleton of the n-dimensional simplex (the higher-dimensional analogue of K_{n+1}) embeds in R^{2k} if and only if n is less or equal to 2k+2. Two decades ago, Kuhnel conjectured that the k-skeleton of the n-simplex embeds in a compact, (k-1)-connected 2k-manifold with kth Z_2-Betti number b_k only if the following generalized Heawood inequality holds: binom{n-k-1}{k+1} is at most binom{2k+1}{k+1} b_k. This is a common generalization of the case of graphs on surfaces as well as the Van Kampen--Flores theorem. In the spirit of Kuhnel's conjecture, we prove that if the k-skeleton of the n-simplex embeds in a 2k-manifold with kth Z_2-Betti number b_k, then n is at most 2b_k binom{2k+2}{k} + 2k + 5. This bound is weaker than the generalized Heawood inequality, but does not require the assumption that M is (k-1)-connected. Our proof uses a result of Volovikov about maps that satisfy a certain homological triviality condition.},
  author       = {Goaoc, Xavier and Mabillard, Isaac and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli},
  location     = {Eindhoven, Netherlands},
  pages        = {476 -- 490},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{On generalized Heawood inequalities for manifolds: A Van Kampen–Flores-type nonembeddability result}},
  doi          = {10.4230/LIPIcs.SOCG.2015.476},
  volume       = {34 },
  year         = {2015},
}

@inproceedings{1512,
  abstract     = {We show that very weak topological assumptions are enough to ensure the existence of a Helly-type theorem. More precisely, we show that for any non-negative integers b and d there exists an integer h(b,d) such that the following holds. If F is a finite family of subsets of R^d such that the ith reduced Betti number (with Z_2 coefficients in singular homology) of the intersection of any proper subfamily G of F is at most b for every non-negative integer i less or equal to (d-1)/2, then F has Helly number at most h(b,d). These topological conditions are sharp: not controlling any of these first Betti numbers allow for families with unbounded Helly number. Our proofs combine homological non-embeddability results with a Ramsey-based approach to build, given an arbitrary simplicial complex K, some well-behaved chain map from C_*(K) to C_*(R^d). Both techniques are of independent interest.},
  author       = {Goaoc, Xavier and Paták, Pavel and Patakova, Zuzana and Tancer, Martin and Wagner, Uli},
  location     = {Eindhoven, Netherlands},
  pages        = {507 -- 521},
  publisher    = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
  title        = {{Bounding Helly numbers via Betti numbers}},
  doi          = {10.4230/LIPIcs.SOCG.2015.507},
  volume       = {34},
  year         = {2015},
}

@article{1513,
  abstract     = {Insects of the order Hemiptera (true bugs) use a wide range of mechanisms of sex determination, including genetic sex determination, paternal genome elimination, and haplodiploidy. Genetic sex determination, the prevalent mode, is generally controlled by a pair of XY sex chromosomes or by an XX/X0 system, but different configurations that include additional sex chromosomes are also present. Although this diversity of sex determining systems has been extensively studied at the cytogenetic level, only the X chromosome of the model pea aphid Acyrthosiphon pisum has been analyzed at the genomic level, and little is known about X chromosome biology in the rest of the order.

In this study, we take advantage of published DNA- and RNA-seq data from three additional Hemiptera species to perform a comparative analysis of the gene content and expression of the X chromosome throughout this clade. We find that, despite showing evidence of dosage compensation, the X chromosomes of these species show female-biased expression, and a deficit of male-biased genes, in direct contrast to the pea aphid X. We further detect an excess of shared gene content between these very distant species, suggesting that despite the diversity of sex determining systems, the same chromosomal element is used as the X throughout a large portion of the order. },
  author       = {Pal, Arka and Vicoso, Beatriz},
  journal      = {Genome Biology and Evolution},
  number       = {12},
  pages        = {3259 -- 3268},
  publisher    = {Oxford University Press},
  title        = {{The X chromosome of hemipteran insects: Conservation, dosage compensation and sex-biased expression}},
  doi          = {10.1093/gbe/evv215},
  volume       = {7},
  year         = {2015},
}

@article{1514,
  abstract     = {Endocannabinoids (eCBs) play key roles in brain function, acting as modulatory signals in synaptic transmission and plasticity. They are recognized as retrograde messengers that mediate long-term synaptic depression (LTD), but their ability to induce long-term potentiation (LTP) is poorly known. We show that eCBs induce the long-term enhancement of transmitter release at single hippocampal synapses through stimulation of astrocytes when coincident with postsynaptic activity. This LTP requires the coordinated activity of the 3 elements of the tripartite synapse: 1) eCB-evoked astrocyte calcium signal that stimulates glutamate release; 2) postsynaptic nitric oxide production; and 3) activation of protein kinase C and presynaptic group I metabotropic glutamate receptors, whose location at presynaptic sites was confirmed by immunoelectron microscopy. Hence, while eCBs act as retrograde signals to depress homoneuronal synapses, they serve as lateral messengers to induce LTP in distant heteroneuronal synapses through stimulation of astrocytes. Therefore, eCBs can trigger LTP through stimulation of astrocyte-neuron signaling, revealing novel cellular mechanisms of eCB effects on synaptic plasticity.},
  author       = {Gómez-Gonzalo, Marta and Navarrete, Marta and Perea, Gertrudis and Covelo, Ana and Martín-Fernández, Mario and Ryuichi Shigemoto and Luján, Rafael and Araque, Alfonso},
  journal      = {Cerebral Cortex},
  number       = {10},
  pages        = {3699 -- 3712},
  publisher    = {Oxford University Press},
  title        = {{Endocannabinoids induce lateral long term potentiation of transmitter release by stimulation of gliotransmission}},
  doi          = {10.1093/cercor/bhu231},
  volume       = {25},
  year         = {2015},
}

@article{1515,
  abstract     = {Type 1 metabotropic glutamate (mGlu1) receptors play a pivotal role in different forms of synaptic plasticity in the cerebellar cortex, e.g. long-term depression at glutamatergic synapses and rebound potentiation at GABAergic synapses. These various forms of plasticity might depend on the subsynaptic arrangement of the receptor in Purkinje cells that can be regulated by protein-protein interactions. This study investigated, by means of the freeze-fracture replica immunogold labelling method, the subcellular localization of mGlu1 receptors in the rodent cerebellum and whether Homer proteins regulate their subsynaptic distribution. We observed a widespread extrasynaptic localization of mGlu1 receptors and confirmed their peri-synaptic enrichment at glutamatergic synapses. Conversely, we detected mGlu1 receptors within the main body of GABAergic synapses onto Purkinje cell dendrites. Although Homer proteins are known to interact with the mGlu1 receptor C-terminus, we could not detect Homer3, the most abundant Homer protein in the cerebellar cortex, at GABAergic synapses by pre-embedding and post-embedding immunoelectron microscopy. We then hypothesized a critical role for Homer proteins in the peri-junctional localization of mGlu1 receptors at glutamatergic synapses. To disrupt Homer-associated protein complexes, mice were tail-vein injected with the membrane-permeable dominant-negative TAT-Homer1a. Freeze-fracture replica immunogold labelling analysis showed no significant alteration in the mGlu1 receptor distribution pattern at parallel fibre-Purkinje cell synapses, suggesting that other scaffolding proteins are involved in the peri-synaptic confinement. The identification of interactors that regulate the subsynaptic localization of the mGlu1 receptor at neurochemically distinct synapses may offer new insight into its trafficking and intracellular signalling.},
  author       = {Mansouri, Mahnaz and Kasugai, Yu and Fukazawa, Yugo and Bertaso, Federica and Raynaud, Fabrice and Perroy, Julie and Fagni, Laurent and Walter Kaufmann and Watanabe, Masahiko and Ryuichi Shigemoto and Ferraguti, Francesco},
  journal      = {European Journal of Neuroscience},
  number       = {2},
  pages        = {157 -- 167},
  publisher    = {Wiley-Blackwell},
  title        = {{Distinct subsynaptic localization of type 1 metabotropic glutamate receptors at glutamatergic and GABAergic synapses in the rodent cerebellar cortex}},
  doi          = {10.1111/ejn.12779},
  volume       = {41},
  year         = {2015},
}

@article{1517,
  abstract     = {We study the large deviation rate functional for the empirical distribution of independent Brownian particles with drift. In one dimension, it has been shown by Adams, Dirr, Peletier and Zimmer that this functional is asymptotically equivalent (in the sense of Γ-convergence) to the Jordan-Kinderlehrer-Otto functional arising in the Wasserstein gradient flow structure of the Fokker-Planck equation. In higher dimensions, part of this statement (the lower bound) has been recently proved by Duong, Laschos and Renger, but the upper bound remained open, since the proof of Duong et al relies on regularity properties of optimal transport maps that are restricted to one dimension. In this note we present a new proof of the upper bound, thereby generalising the result of Adams et al to arbitrary dimensions.
},
  author       = {Erbar, Matthias and Maas, Jan and Renger, Michiel},
  journal      = {Electronic Communications in Probability},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{From large deviations to Wasserstein gradient flows in multiple dimensions}},
  doi          = {10.1214/ECP.v20-4315},
  volume       = {20},
  year         = {2015},
}

@article{1519,
  abstract     = {Evolutionary biologists have an array of powerful theoretical techniques that can accurately predict changes in the genetic composition of populations. Changes in gene frequencies and genetic associations between loci can be tracked as they respond to a wide variety of evolutionary forces. However, it is often less clear how to decompose these various forces into components that accurately reflect the underlying biology. Here, we present several issues that arise in the definition and interpretation of selection and selection coefficients, focusing on insights gained through the examination of selection coefficients in multilocus notation. Using this notation, we discuss how its flexibility-which allows different biological units to be identified as targets of selection-is reflected in the interpretation of the coefficients that the notation generates. In many situations, it can be difficult to agree on whether loci can be considered to be under "direct" versus "indirect" selection, or to quantify this selection. We present arguments for what the terms direct and indirect selection might best encompass, considering a range of issues, from viability and sexual selection to kin selection. We show how multilocus notation can discriminate between direct and indirect selection, and describe when it can do so.},
  author       = {Barton, Nicholas H and Servedio, Maria},
  journal      = {Evolution},
  number       = {5},
  pages        = {1101 -- 1112},
  publisher    = {Wiley},
  title        = {{The interpretation of selection coefficients}},
  doi          = {10.1111/evo.12641},
  volume       = {69},
  year         = {2015},
}

@inproceedings{1520,
  abstract     = {Creating mechanical automata that can walk in stable and pleasing manners is a challenging task that requires both skill and expertise. We propose to use computational design to offset the technical difficulties of this process. A simple drag-and-drop interface allows casual users to create personalized walking toys from a library of pre-defined template mechanisms. Provided with this input, our method leverages physical simulation and evolutionary optimization to refine the mechanical designs such that the resulting toys are able to walk. The optimization process is guided by an intuitive set of objectives that measure the quality of the walking motions. We demonstrate our approach on a set of simulated mechanical toys with different numbers of legs and various distinct gaits. Two fabricated prototypes showcase the feasibility of our designs.},
  author       = {Bharaj, Gaurav and Coros, Stelian and Thomaszewski, Bernhard and Tompkin, James and Bickel, Bernd and Pfister, Hanspeter},
  isbn         = {978-1-4503-3496-9},
  location     = {Los Angeles, CA, United States},
  pages        = {93 -- 100},
  publisher    = {ACM},
  title        = {{Computational design of walking automata}},
  doi          = {10.1145/2786784.2786803},
  year         = {2015},
}

@article{1525,
  abstract     = {Based on 16 recommendations, efforts should be made to achieve the following goal: By 2025, all scholarly publication activity in Austria should be Open Access. In other words, the final versions of all scholarly publications resulting from the support of public resources must be freely accessible on the Internet without delay (Gold Open Access). The resources required to meet this obligation shall be provided to the authors, or the cost of the publication venues shall be borne directly by the research organisations.},
  author       = {Bauer, Bruno and Blechl, Guido and Bock, Christoph and Danowski, Patrick and Ferus, Andreas and Graschopf, Anton and König, Thomas and Mayer, Katja and Reckling, Falk and Rieck, Katharina and Seitz, Peter and Stöger, Herwig and Welzig, Elvira},
  journal      = {VÖB Mitteilungen},
  number       = {3},
  pages        = {580 -- 607},
  publisher    = {Verein Österreichischer Bibliothekare},
  title        = {{Arbeitsgruppe „Nationale Strategie“ des Open Access Network Austria OANA}},
  doi          = {10.5281/zenodo.33178},
  volume       = {68},
  year         = {2015},
}

@article{1530,
  abstract     = {In growing cells, protein synthesis and cell growth are typically not synchronous, and, thus, protein concentrations vary over the cell division cycle. We have developed a theoretical description of genetic regulatory systems in bacteria that explicitly considers the cell division cycle to investigate its impact on gene expression. We calculate the cell-to-cell variations arising from cells being at different stages in the division cycle for unregulated genes and for basic regulatory mechanisms. These variations contribute to the extrinsic noise observed in single-cell experiments, and are most significant for proteins with short lifetimes. Negative autoregulation buffers against variation of protein concentration over the division cycle, but the effect is found to be relatively weak. Stronger buffering is achieved by an increased protein lifetime. Positive autoregulation can strongly amplify such variation if the parameters are set to values that lead to resonance-like behaviour. For cooperative positive autoregulation, the concentration variation over the division cycle diminishes the parameter region of bistability and modulates the switching times between the two stable states. The same effects are seen for a two-gene mutual-repression toggle switch. By contrast, an oscillatory circuit, the repressilator, is only weakly affected by the division cycle.},
  author       = {Bierbaum, Veronika and Klumpp, Stefan},
  journal      = {Physical Biology},
  number       = {6},
  publisher    = {IOP Publishing Ltd.},
  title        = {{Impact of the cell division cycle on gene circuits}},
  doi          = {10.1088/1478-3975/12/6/066003},
  volume       = {12},
  year         = {2015},
}

@inbook{1531,
  abstract     = {The Heat Kernel Signature (HKS) is a scalar quantity which is derived from the heat kernel of a given shape. Due to its robustness, isometry invariance, and multiscale nature, it has been successfully applied in many geometric applications. From a more general point of view, the HKS can be considered as a descriptor of the metric of a Riemannian manifold. Given a symmetric positive definite tensor field we may interpret it as the metric of some Riemannian manifold and thereby apply the HKS to visualize and analyze the given tensor data. In this paper, we propose a generalization of this approach that enables the treatment of indefinite tensor fields, like the stress tensor, by interpreting them as a generator of a positive definite tensor field. To investigate the usefulness of this approach we consider the stress tensor from the two-point-load model example and from a mechanical work piece.},
  author       = {Zobel, Valentin and Reininghaus, Jan and Hotz, Ingrid},
  booktitle    = {Visualization and Processing of Higher Order Descriptors for Multi-Valued Data},
  editor       = {Hotz, Ingrid and Schultz, Thomas},
  isbn         = {978-3-319-15089-5},
  pages        = {257 -- 267},
  publisher    = {Springer},
  title        = {{Visualizing symmetric indefinite 2D tensor fields using The Heat Kernel Signature}},
  doi          = {10.1007/978-3-319-15090-1_13},
  volume       = {40},
  year         = {2015},
}

@article{1532,
  abstract     = {Ammonium is the major nitrogen source in some plant ecosystems but is toxic at high concentrations, especially when available as the exclusive nitrogen source. Ammonium stress rapidly leads to various metabolic and hormonal imbalances that ultimately inhibit root and shoot growth in many plant species, including Arabidopsis thaliana (L.) Heynh. To identify molecular and genetic factors involved in seedling survival with prolonged exclusive NH4+ nutrition, a transcriptomic analysis with microarrays was used. Substantial transcriptional differences were most pronounced in (NH4)2SO4-grown seedlings, compared with plants grown on KNO3 or NH4NO3. Consistent with previous physiological analyses, major differences in the expression modules of photosynthesis-related genes, an altered mitochondrial metabolism, differential expression of the primary NH4+ assimilation, alteration of transporter gene expression and crucial changes in cell wall biosynthesis were found. A major difference in plant hormone responses, particularly of auxin but not cytokinin, was striking. The activity of the DR5::GUS reporter revealed a dramatically decreased auxin response in (NH4)2SO4-grown primary roots. The impaired root growth on (NH4)2SO4 was partially rescued by exogenous auxin or in specific mutants in the auxin pathway. The data suggest that NH4+-induced nutritional and metabolic imbalances can be partially overcome by elevated auxin levels.},
  author       = {Yang, Huaiyu and Von Der Fecht Bartenbach, Jenny and Friml, Jirí and Lohmann, Jan and Neuhäuser, Benjamin and Ludewig, Uwe},
  issn         = {1445-4408},
  journal      = {Functional Plant Biology},
  number       = {3},
  pages        = {239 -- 251},
  publisher    = {CSIRO},
  title        = {{Auxin-modulated root growth inhibition in Arabidopsis thaliana seedlings with ammonium as the sole nitrogen source}},
  doi          = {10.1071/FP14171},
  volume       = {42},
  year         = {2015},
}

@article{1533,
  abstract     = {This paper addresses the problem of semantic segmentation, where the possible class labels are from a predefined set. We exploit top-down guidance, i.e., the coarse localization of the objects and their class labels provided by object detectors. For each detected bounding box, figure-ground segmentation is performed and the final result is achieved by merging the figure-ground segmentations. The main idea of the proposed approach, which is presented in our preliminary work, is to reformulate the figure-ground segmentation problem as sparse reconstruction pursuing the object mask in a nonparametric manner. The latent segmentation mask should be coherent subject to sparse error caused by intra-category diversity; thus, the object mask is inferred by making use of sparse representations over the training set. To handle local spatial deformations, local patch-level masks are also considered and inferred by sparse representations over the spatially nearby patches. The sparse reconstruction coefficients and the latent mask are alternately optimized by applying the Lasso algorithm and the accelerated proximal gradient method. The proposed formulation results in a convex optimization problem; thus, the global optimal solution is achieved. In this paper, we provide theoretical analysis of the convergence and optimality. We also give an extended numerical analysis of the proposed algorithm and a comprehensive comparison with the related semantic segmentation methods on the challenging PASCAL visual object class object segmentation datasets and the Weizmann horse dataset. The experimental results demonstrate that the proposed algorithm achieves a competitive performance when compared with the state of the arts.},
  author       = {Xia, Wei and Domokos, Csaba and Xiong, Junjun and Cheong, Loongfah and Yan, Shuicheng},
  journal      = {IEEE Transactions on Circuits and Systems for Video Technology},
  number       = {8},
  pages        = {1295 -- 1308},
  publisher    = {IEEE},
  title        = {{Segmentation over detection via optimal sparse reconstructions}},
  doi          = {10.1109/TCSVT.2014.2379972},
  volume       = {25},
  year         = {2015},
}

@article{1534,
  abstract     = {PIN proteins are auxin export carriers that direct intercellular auxin flow and in turn regulate many aspects of plant growth and development including responses to environmental changes. The Arabidopsis R2R3-MYB transcription factor FOUR LIPS (FLP) and its paralogue MYB88 regulate terminal divisions during stomatal development, as well as female reproductive development and stress responses. Here we show that FLP and MYB88 act redundantly but differentially in regulating the transcription of PIN3 and PIN7 in gravity-sensing cells of primary and lateral roots. On the one hand, FLP is involved in responses to gravity stimulation in primary roots, whereas on the other, FLP and MYB88 function complementarily in establishing the gravitropic set-point angles of lateral roots. Our results support a model in which FLP and MYB88 expression specifically determines the temporal-spatial patterns of PIN3 and PIN7 transcription that are closely associated with their preferential functions during root responses to gravity.},
  author       = {Wang, Hongzhe and Yang, Kezhen and Zou, Junjie and Zhu, Lingling and Xie, Zidian and Morita, Miyoterao and Tasaka, Masao and Friml, Jirí and Grotewold, Erich and Beeckman, Tom and Vanneste, Steffen and Sack, Fred and Le, Jie},
  journal      = {Nature Communications},
  publisher    = {Nature Publishing Group},
  title        = {{Transcriptional regulation of PIN genes by FOUR LIPS and MYB88 during Arabidopsis root gravitropism}},
  doi          = {10.1038/ncomms9822},
  volume       = {6},
  year         = {2015},
}

@article{1535,
  abstract     = {Neuronal and neuroendocrine L-type calcium channels (Cav1.2, Cav1.3) open readily at relatively low membrane potentials and allow Ca2+ to enter the cells near resting potentials. In this way, Cav1.2 and Cav1.3 shape the action potential waveform, contribute to gene expression, synaptic plasticity, neuronal differentiation, hormone secretion and pacemaker activity. In the chromaffin cells (CCs) of the adrenal medulla, Cav1.3 is highly expressed and is shown to support most of the pacemaking current that sustains action potential (AP) firings and part of the catecholamine secretion. Cav1.3 forms Ca2+-nanodomains with the fast inactivating BK channels and drives the resting SK currents. These latter set the inter-spike interval duration between consecutive spikes during spontaneous firing and the rate of spike adaptation during sustained depolarizations. Cav1.3 plays also a primary role in the switch from “tonic” to “burst” firing that occurs in mouse CCs when either the availability of voltage-gated Na channels (Nav) is reduced or the β2 subunit featuring the fast inactivating BK channels is deleted. Here, we discuss the functional role of these “neuronlike” firing modes in CCs and how Cav1.3 contributes to them. The open issue is to understand how these novel firing patterns are adapted to regulate the quantity of circulating catecholamines during resting condition or in response to acute and chronic stress.},
  author       = {Vandael, David H and Marcantoni, Andrea and Carbone, Emilio},
  journal      = {Current Molecular Pharmacology},
  number       = {2},
  pages        = {149 -- 161},
  publisher    = {Bentham Science Publishers},
  title        = {{Cav1.3 channels as key regulators of neuron-like firings and catecholamine release in chromaffin cells}},
  doi          = {10.2174/1874467208666150507105443},
  volume       = {8},
  year         = {2015},
}

@article{1536,
  abstract     = {Strigolactones, first discovered as germination stimulants for parasitic weeds [1], are carotenoid-derived phytohormones that play major roles in inhibiting lateral bud outgrowth and promoting plant-mycorrhizal symbiosis [2-4]. Furthermore, strigolactones are involved in the regulation of lateral and adventitious root development, root cell division [5, 6], secondary growth [7], and leaf senescence [8]. Recently, we discovered the strigolactone transporter Petunia axillaris PLEIOTROPIC DRUG RESISTANCE 1 (PaPDR1), which is required for efficient mycorrhizal colonization and inhibition of lateral bud outgrowth [9]. However, how strigolactones are transported through the plant remained unknown. Here we show that PaPDR1 exhibits a cell-type-specific asymmetric localization in different root tissues. In root tips, PaPDR1 is co-expressed with the strigolactone biosynthetic gene DAD1 (CCD8), and it is localized at the apical membrane of root hypodermal cells, presumably mediating the shootward transport of strigolactone. Above the root tip, in the hypodermal passage cells that form gates for the entry of mycorrhizal fungi, PaPDR1 is present in the outer-lateral membrane, compatible with its postulated function as strigolactone exporter from root to soil. Transport studies are in line with our localization studies since (1) a papdr1 mutant displays impaired transport of strigolactones out of the root tip to the shoot as well as into the rhizosphere and (2) DAD1 expression and PIN1/PIN2 levels change in plants deregulated for PDR1 expression, suggestive of variations in endogenous strigolactone contents. In conclusion, our results indicate that the polar localizations of PaPDR1 mediate directional shootward strigolactone transport as well as localized exudation into the soil.},
  author       = {Sasse, Joëlle and Simon, Sibu and Gübeli, Christian and Liu, Guowei and Cheng, Xi and Friml, Jirí and Bouwmeester, Harro and Martinoia, Enrico and Borghi, Lorenzo},
  journal      = {Current Biology},
  number       = {5},
  pages        = {647 -- 655},
  publisher    = {Cell Press},
  title        = {{Asymmetric localizations of the ABC transporter PaPDR1 trace paths of directional strigolactone transport}},
  doi          = {10.1016/j.cub.2015.01.015},
  volume       = {25},
  year         = {2015},
}

@article{1537,
  abstract     = {3D amoeboid cell migration is central to many developmental and disease-related processes such as cancer metastasis. Here, we identify a unique prototypic amoeboid cell migration mode in early zebrafish embryos, termed stable-bleb migration. Stable-bleb cells display an invariant polarized balloon-like shape with exceptional migration speed and persistence. Progenitor cells can be reversibly transformed into stable-bleb cells irrespective of their primary fate and motile characteristics by increasing myosin II activity through biochemical or mechanical stimuli. Using a combination of theory and experiments, we show that, in stable-bleb cells, cortical contractility fluctuations trigger a stochastic switch into amoeboid motility, and a positive feedback between cortical flows and gradients in contractility maintains stable-bleb cell polarization. We further show that rearward cortical flows drive stable-bleb cell migration in various adhesive and non-adhesive environments, unraveling a highly versatile amoeboid migration phenotype.},
  author       = {Ruprecht, Verena and Wieser, Stefan and Callan Jones, Andrew and Smutny, Michael and Morita, Hitoshi and Sako, Keisuke and Barone, Vanessa and Ritsch Marte, Monika and Sixt, Michael K and Voituriez, Raphaël and Heisenberg, Carl-Philipp J},
  journal      = {Cell},
  number       = {4},
  pages        = {673 -- 685},
  publisher    = {Cell Press},
  title        = {{Cortical contractility triggers a stochastic switch to fast amoeboid cell motility}},
  doi          = {10.1016/j.cell.2015.01.008},
  volume       = {160},
  year         = {2015},
}

@article{1538,
  abstract     = {Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time.},
  author       = {Ruess, Jakob and Parise, Francesca and Milias Argeitis, Andreas and Khammash, Mustafa and Lygeros, John},
  journal      = {PNAS},
  number       = {26},
  pages        = {8148 -- 8153},
  publisher    = {National Academy of Sciences},
  title        = {{Iterative experiment design guides the characterization of a light-inducible gene expression circuit}},
  doi          = {10.1073/pnas.1423947112},
  volume       = {112},
  year         = {2015},
}

@article{1539,
  abstract     = {Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. },
  author       = {Ruess, Jakob},
  journal      = {Journal of Chemical Physics},
  number       = {24},
  publisher    = {American Institute of Physics},
  title        = {{Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space}},
  doi          = {10.1063/1.4937937},
  volume       = {143},
  year         = {2015},
}

@article{1540,
  abstract     = {Plant sexual reproduction involves highly structured and specialized organs: stamens (male) and gynoecia (female, containing ovules). These organs synchronously develop within protective flower buds, until anthesis, via tightly coordinated mechanisms that are essential for effective fertilization and production of viable seeds. The phytohormone auxin is one of the key endogenous signalling molecules controlling initiation and development of these, and other, plant organs. In particular, its uneven distribution, resulting from tightly controlled production, metabolism and directional transport, is an important morphogenic factor. In this review we discuss how developmentally controlled and localized auxin biosynthesis and transport contribute to the coordinated development of plants' reproductive organs, and their fertilized derivatives (embryos) via the regulation of auxin levels and distribution within and around them. Current understanding of the links between de novo local auxin biosynthesis, auxin transport and/or signalling is presented to highlight the importance of the non-cell autonomous action of auxin production on development and morphogenesis of reproductive organs and embryos. An overview of transcription factor families, which spatiotemporally define local auxin production by controlling key auxin biosynthetic enzymes, is also presented.},
  author       = {Robert, Hélène and Crhák Khaitová, Lucie and Mroue, Souad and Benková, Eva},
  journal      = {Journal of Experimental Botany},
  number       = {16},
  pages        = {5029 -- 5042},
  publisher    = {Oxford University Press},
  title        = {{The importance of localized auxin production for morphogenesis of reproductive organs and embryos in Arabidopsis}},
  doi          = {10.1093/jxb/erv256},
  volume       = {66},
  year         = {2015},
}